I've been hunting around the docs and google and can't seem to find the
answer to curiousity I'm having.... I'm trying to set the -F option
(filter query sequence) for blastall in the
Bio::Tools::Run::STandAloneBlast module.
In the module code there's a -filter option in %runParams and in the docs
there's the example:
@params = ('program' => 'blastn', 'database' => 'ecoli.nt');
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
So I try and set 'filter' => 'F' in my code. Unfortunately this causes
bioperl to pass -f F to blastall instead of -F F.
Am I just using the wrong parameter to the module or is this a
capitalization bug? Thanks.
--
Matthew Laird
SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University